Serialization support for BasePairParameters class

luke czapla · luke czapla · commit 8a4ffa80efb5 · 2017-07-26T02:21:44.000-04:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java
@@ -10,6 +10,7 @@
 import javax.vecmath.Point3d;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.io.Serializable;
 import java.util.*;
 
 import org.slf4j.Logger;
@@ -34,8 +35,9 @@
  * @since 5.0.0-snapshot
  *
  */
-public class BasePairParameters {
+public class BasePairParameters implements Serializable {
 
+    private static final long serialVersionUID = 6214502385L;
     private static Logger log = LoggerFactory.getLogger(BasePairParameters.class);
 
     // See URL http://ndbserver.rutgers.edu/ndbmodule/archives/reports/tsukuba/Table1.html
@@ -114,7 +116,7 @@ public class BasePairParameters {
         ringMap.put(3, Arrays.asList("C6", "C2", "N3", "C4", "C5", "N1"));
    }
 
-    protected Structure structure;
+    protected transient Structure structure;
     protected boolean canonical = true;
     protected boolean useRNA = false;
     protected boolean nonredundant = false;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/MismatchedBasePairParameters.java
@@ -7,6 +7,7 @@
 import org.biojava.nbio.structure.contact.Pair;
 
 import javax.vecmath.Matrix4d;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -18,7 +19,7 @@
  * @since 5.0.0-snapshot
  *
  */
-public class MismatchedBasePairParameters extends BasePairParameters {
+public class MismatchedBasePairParameters extends BasePairParameters implements Serializable {
 
     // These are the criteria used to select proper base pairs.
     protected static double MaxStagger = 2.0, MaxShear = 5.0, MaxStretch = 5.0,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/TertiaryBasePairParameters.java
@@ -7,6 +7,7 @@
 import org.biojava.nbio.structure.contact.Pair;
 
 import javax.vecmath.Matrix4d;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -19,7 +20,7 @@
  * @since 5.0.0-snapshot
  *
  */
-public class TertiaryBasePairParameters extends BasePairParameters {
+public class TertiaryBasePairParameters extends BasePairParameters implements Serializable {
 
     // These are the criteria used to select proper base pairs.
     protected static double MaxStagger = 2.0, MaxPropeller = 60.0;
